Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Parameters
• Deployments
• Project Information
• Program Information
• Funding

These metagenomic and metatranscriptomic time-series data cover a 52-day period in the fall of 2016 during an intense bloom of the dinoflagellate Akashiwo sanguinea in Monterey Bay, CA, USA. The dataset comprises 84 metagenomes, 82 metatranscriptomes, and 88 16S rRNA amplicon libraries that capture the functions and taxonomy the bacterial and archaeal community. In addition, 88 18S rRNA amplicon libraries describe the taxonomy of the eukaryotic community during the bloom. Microbial cells were collected at station M0 using the moored autonomous robotic Environmental Sample Processor (ESP) instrument and preserved with RNAlater in the instrument until retrieval.

The Environmental Sample Processor (ESP) filtered seawater sequentially through 5.0 um and 0.2 um pore size polyvinylidene fluoride filters. Seawater was evacuated from filters and followed twice with a 2 minute incubation with 1 ml of RNAlater™. RNAlater was evacuated, and filters were stored in the ESP until they were transferred to -80 C upon instrument recovery. 

Grab samples for sequencing while the ESP was not deployed were taken using Niskin bottles that collected seawater at the same depth and location of the ESP. Water was transferred to a low-density polyethylene cubitainer and maintained at ambient temperature until return to lab within 30 min. Seawater was filtered as above with vacuum filtration and preserved immediately in liquid nitrogen and transferred to -80 C.

Single-cell sequencing: Seawater was transferred directly from the Niskin bottle to a 50 ml Falcon tube and placed on ice until brought back to lab. Each sampling day, 3 x 1 ml of seawater was preserved in cryovials using 100 ul of glyTe (5 ml glycerol, 3 ml Milli-Q H2O, 1 ml 100 x TE pH 8.0, 0.2 um filter sterilized after mixing the above, and stored in -20 C freezer). Preserved samples were then placed in a -80 C freezer. Samples were processed and sequenced at JGI

ESP and grab sample filters were processed for DNA and RNA using the Zymobiomics DNA/RNA Mini Kit. Turbo DNase and RiboZero were performed on RNA samples. Illumina HiSeq-2500 1TB 2 x 151 bp sequencing was performed at the Joint Genome Institute (JGI). 

BBtools was used to trim and screen reads, followed by read correction using bfc (version r181). Reads with no mate pair were removed. Metagenomes were assembled using SPAdes assembler 3.11.1. The entire filtered read set was mapped to the final assembly and coverage information generated using bbmap (version 37.78). Metatranscriptomes were assembled using MEGAHIT v1.1.2 and reads were mapped to the assembly using BBMap. The JGI Integrated Microbial Genomes System (IMG) was used for annotation of the metagenomes and metatranscriptomes.

BCO-DMO Processing notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- reformatted date from Mon-DD (Oct-04) to YYYYMMDD (20141004)

Surface ocean bacterioplankton preside over a divergence point in the marine sulfur cycle where the fate of dimethylsulfoniopropionate (DMSP) is determined. While it is well recognized that this juncture influences the fate of sulfur in the ocean and atmosphere, its regulation by bacterioplankton is not yet understood. Based on recent findings in biogeochemistry, bacterial physiology, bacterial genetics, and ocean instrumentation, the microbial oceanography community is poised to make major advances in knowledge of this control point. This research project is ascertaining how the major taxa of bacterial DMSP degraders in seawater regulate DMSP transformations, and addresses the implications of bacterial functional, genetic, and taxonomic diversity for global sulfur cycling.

The project is founded on the globally important function of bacterial transformation of the ubiquitous organic sulfur compound DMSP in ocean surface waters. Recent genetic discoveries have identified key genes in the two major DMSP degradation pathways, and the stage is now set to identify the factors that regulate gene expression to favor one or the other pathway during DMSP processing. The taxonomy of the bacteria mediating DMSP cycling has been deduced from genomic and metagenomic sequencing surveys to include four major groups of surface ocean bacterioplankton. How regulation of DMSP degradation differs among these groups and maps to phylogeny in co-occurring members is key information for understanding the marine sulfur cycle and predicting its function in a changing ocean. Using model organism studies, microcosm experiments (at Dauphin Island Sea Lab, AL), and time-series field studies with an autonomous sample collection instrument (at Monterey Bay, CA), this project is taking a taxon-specific approach to decipher the regulation of bacterial DMSP degradation.

This research addresses fundamental questions of how the diversity of microbial life influences the geochemical environment of the oceans and atmosphere, linking the genetic basis of metabolic potential to taxonomic diversity. The project is training graduate students and post-doctoral scholars in microbial biodiversity and providing research opportunities and mentoring for undergraduate students. An outreach program is enhance understanding of the role and diversity of marine microorganisms in global elemental cycles among high school students. Advanced Placement Biology students are participating in marine microbial research that covers key learning goals in the AP Biology curriculum. Two high school students are selected each year for summer research internships in PI laboratories.

(adapted from the NSF Synopsis of Program)
Dimensions of Biodiversity is a program solicitation from the NSF Directorate for Biological Sciences. FY 2010 was year one of the program.  [MORE from NSF]

The NSF Dimensions of Biodiversity program seeks to characterize biodiversity on Earth by using integrative, innovative approaches to fill rapidly the most substantial gaps in our understanding. The program will take a broad view of biodiversity, and in its initial phase will focus on the integration of genetic, taxonomic, and functional dimensions of biodiversity. Project investigators are encouraged to integrate these three dimensions to understand the interactions and feedbacks among them. While this focus complements several core NSF programs, it differs by requiring that multiple dimensions of biodiversity be addressed simultaneously, to understand the roles of biodiversity in critical ecological and evolutionary processes.